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Old 01-11-2015, 08:54 PM   #1
vcc
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Join Date: Apr 2011
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Default Bowtie output variability

Hello everyone,

I have used Bowtie many a times earlier, but was not trapped in such situation as given below:

I have query related to bowtie output.
1. When I am using bowtie with options (bowtie -a -p 32 <index> -1 reads1 -2 reads2 --phred33 -X 250 out.sam), I am getting the following output:
# reads processed: 2357373
# reads with at least one reported alignment: 1992781 (84.53%)
# reads that failed to align: 364592 (15.47%)
Reported 9698140 paired-end alignments to 1 output stream(s)

2. and when I am using bowtie for same index and initial reads with options (bowtie -a -m 1 -p 32 <index> -1 reads1 -2 reads2 --phred33 -X 250 --al paired-all-ref.fastq --max paired-align-ref-max.fastq out.sam
# reads processed: 2357373
# reads with at least one reported alignment: 422462 (17.92%)
# reads that failed to align: 1345003 (57.06%)
# reads with alignments suppressed due to -m: 589908 (25.02%)
Reported 422462 paired-end alignments to 1 output stream(s)

From first and second you could see that there is high variation in aligned/unaligned total number of reads. Could anyone please guide me why this is happening.
I need to extract paired end reads mapping more than one time. But these variations in output is confusing me.

Also the reads length are 25 to 28 bases for each pair.
Can I use Bowtie2, for such short reads.
I also tried the the same with following options:
bowtie2 -x <index> -q -1 reads1 -2 reads2 -p 32 --end-to-end --no-mixed --no-discordant -X 250 --no-unal -S out.sam
and getting following output:
2357373 reads; of these:
2357373 (100.00%) were paired; of these:
350824 (14.88%) aligned concordantly 0 times
404316 (17.15%) aligned concordantly exactly 1 time
1602233 (67.97%) aligned concordantly >1 times
85.12% overall alignment rate

It will be great if someone could help me out as soon as possible.

Thanks
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bowtie, ngs, reads mapping, short reads

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